If you are interested please have a look at www.dnabarcodingcourses.com. The site details course content, tuition fees, requirements, etc. If you know somebody who might be interested please forward the information.

Thursday, October 29, 2015

While there is no doubt that climate change is affecting many organisms, some species might be more sensitive than others. Reptiles, whose body temperature depends directly on environmental temperature, may be particularly vulnerable.

In a new study, European researchers examined the consequences of a 2°C warmer climate on the persistence of populations of common lizards (Zootoca vivipara), a widespread European reptile.

The team used the Metatron a system of semi-natural enclosures in which temperature can be manipulated to create two distinct climates: one similar to the present climate and another 2 °C warmer, corresponding to the predicted climate for the end of the century. Eighteen populations of common lizards were put into Metatron enclosures over two years in the "present" or "warmed" climate. Populations were surveyed for one year, allowing the team to determine the impact of warmer climates on demographic parameters such as growth rate, reproduction and survival.

Their results show that many common lizard populations could disappear rapidly as a consequence of such warmer temperatures.

While a two-degrees warmer climate might seem beneficial at first, as it leads to faster growth of juvenile lizards and earlier access to reproduction, it also leads to lower survival in adult individuals, which should endanger population survival.Although these results might seem dramatic, we do not predict extinction of common lizards at the scale of the species, but we suggest that populations at the southern edge of their range of distribution might particularly suffer from warmer climates.

A model of population dynamics showed that the increased adult mortality would lead to decreased population growth rates, and ultimately to rapid population extinctions in around 20 years. Comparisons of experimental conditions to climatic conditions encountered by European populations of common lizards show that warmer climates might threaten between 14 and 30 % of European populations depending on the carbon emission scenario.

Anecdotally, we also showed that warmer climates led some adult females to engage into a second reproduction event during the summer, while these lizards normally reproduce only once a year during the spring. Combined with the earlier juvenile reproduction and the higher adult survival, these results suggest a shift of demographic strategy from a relatively long life and low reproductive output to a faster life, higher reproductive investment. We can wonder whether this strategy shift may help adaptation of populations to warmer climates over time.

Wednesday, October 28, 2015

Understanding how new life forms originate is a central question in biology. Population divergence is usually studied with respect to how single lineages diverge into daughter taxa. However, populations may not always differentiate in isolation; divergence of one taxon could create new niche opportunities in higher trophic levels, leading to the sequential origin of many new taxa.

Recent research by a team of US scientists finds that evolutionary changes, in this case in a new species of fruit fly, have an almost domino effect on a number of species. The apple maggot flies evolved into new species when they began laying their eggs and mating on apple trees, as opposed to their native hawthorn tree hosts.

Three different kinds of parasitoid wasps were collected from a number of different fly host plant environments in the wild. Analyses in the lab showed that all three of the different kinds of wasps had diverged from others of the same kind, both genetically and with respect to host-associated physiology and behavior. These evolutionary changes, known as "sequential" or "cascading" events, may provide additional information helping explain why some groups of organisms, such as plants, the insects that feed on them and the parasites that attack the insects, are more diverse and species-rich than other groups.

The new study extends the earlier work by showing that new fruit fly species provide suitable habitat not just for one new parasitoid species, but for multiple new species. In a sense they have caught an entire community of parasitoids actively ecologically diverging in response to a historically documented host plant shift of their fly host.

The catfish Clarias gariepinus is an important aquaculture species because of its rapid growth rate and resistance to handling and stress. In many African countries, C. gariepinus is an important solution to the increasing demand for fish and fish products in response to rapid human population growth, the declining productivity of capture fisheries, and the fear of animal-related disease outbreaks (e.g., avian, bovine, and swine influenza). This has made the catfish a potentially important source of protein and economic growth in many rural and urban communities involved in the fishery industry.

However, the catfish is host to several parasites that might threaten its viability especially in captivity. One of those parasites is the flatworm Tylodelphys mashonense, whose resting larvae occur in the cranial cavity of the fish. The species goes through three hosts during his life cycle. An intermediate snail host and the fish would be its second intermediate host before it moves to its final bird host. Unfortunately, details of this life cycle are poorly understood. The intermediate snail host(s) remain unknown and the range of avian hosts is also not well characterized, apart from the grey heron Ardea cinerea, the type host.

An international team of researchers now used DNA barcoding to link cercariae and sporocysts with adults and metacercariae collected in Tanzania (both Mindu Dam, Morogoro, and Mwanza Gulf, Lake Victoria). Sequences from cercariae infecting Bulinus spp. matched those acquired from metacercariae from Clarias gariepinus, and those from adult Tylodelphys mashonense from the grey heron Ardea cinerea and the white egret Egretta alba.

In conclusion, the successful linking of the life cycle stages of T. mashonense from the Tanzanian freshwater bodies using molecular tools has underlined the usefulness of this approach in unravelling the complex life cycles of digenetic trematodes in the absence of experimental establishment. As a consequence, the control of Tylodelphys species parasitizing C. gariepinus, one of the most suitable species for aquaculture, may become possible.

Monday, October 26, 2015

The small herb Phyllanthus amarus belings to the spurge family Euphorbiaceae. It is is an important plant of several traditional Asian medicines such as the Indian Ayurvedic system, the traditional Thai medicine or the chinese herbal medicine. It is used for a variety of problems with stomach, urogenital system, liver, kidney and spleen. Supposedly extracts from some Phylllanthus species contain biologically active compounds responsible for liver protection from any toxic substances which makes these plants and their extracts a well sought after commodity. However, there are about 1000 species with varying combinations of chemical constituents making it rather confusing. And it gets worse.

For example, Phyllanthus amarus that can be found throughout Thailand and is known in Thai under the vernacular name “Look Tai Bai” (ลูกใต้ใบ) meaning “seeds under leaf”. However, several other species of same genus share this name due morphological similarities, mostly the presence of seeds under the leaves. Therefore, plant material of Phyllanthus amarus picked by a layperson may result in the collection of additional undesired species and thereby causing the end product to be of inferior quality. The plant material is subsequently processed to powder form for capsules or tea rendering any morphological identification impossible.

This method proved to be a very sensitive tool that can be used for rapid detection of contamination as low as 1% of other Phyllanthus species in P. amarus admixtures. All commercial products of P. amarus obtained from a local market in Thailand were found to contain pure raw materials of P. amarus without any substitution or contamination.

The group also found that the use of trnL DNA barcoding coupled with HRM analysis (more and more referred to as bar-HRM) proved to be the most effective method for differentiating Phyllanthus amarus from its congeners, which is especially useful for determining any unwanted plant ingredients in commercial medicinal products. The combination of DNA Barcoding and HRM also reduces cost and time (4 h) in comparison with standard sequence based DNA Barcoding.

The information the citizen scientists gathered shows birds respond to changing conditions in different seasons of the year. While some species benefit from these changes, birds that are adapted to colder regions stand to lose. For example, the study found warmer winters benefit resident birds, such as the Short-toed treecreeper and the Collared Dove, with more productive spring times benefiting short-distance migrants such as the Goldfinch and the Woodlark. Warmer or more productive periods complemented the early or peak breeding season for these birds.

We found benefits from conditions observed under climate change for both resident birds, short-distance migrants and long distance-migrants, but at very different times of the year that complement their breeding season. So if we are to predict what the future bird community may look like in Europe, we need to understand how the conditions during breeding will change.

However, the positive effects mentioned above do not extend to species adapted to the colder regions in Europe, such as the resident birds House Sparrow and Carrion Crow and the short-distance migrants Meadow Pipit and Redpoll. They have become relatively less abundant under the respective conditions. Birds arriving to Europe from furthest away (and therefore later in the year), such as long-distance migrants the Northern Wheatear and Common Redstart, generally benefit from warmer summers in Europe. As a group, however, they showed one of the most complex responses as they are also impacted by climate change in Africa.

Unfortunately, the study also shows the widespread long-term effects of agricultural intensification in Europe, where farmland birds continue to be in decline. It found long-distance migrants may be particularly vulnerable to the combination of agricultural intensification and climate change.

Of course climate change will favour some species, but studies suggest we will have more losers than winners. Long-distance migrants are already believed to be particularly vulnerable to climate change, as they experience impacts in multiple locations along their busy travel routes that stretch two continents. We found that long-distance migrants in particular were in decline in countries with intensive agriculture expressed through high cereal yields. Our results suggest that we should take action to protect long-distance migrant birds in countries with the most intensified agriculture.

Thursday, October 22, 2015

As part of nature's evolutionary arms race, animals have evolved an arsenal of different defense mechanisms, including chemical weapons, such as poisons or irritants, camouflage, warning coloration and mimicry. The ways these mechanisms deter predators have been well studied, but little is known about how they might impact evolutionary processes such as speciation and extinction.

In a large-scale empirical test in amphibians that use toxins to protect themselves against predators, scientists at the University of Liverpool examined how rates of extinction and speciation varied across different defensive traits in amphibians. They found that animals that use chemical defense show higher rates of speciation, but also higher rates of extinction, compared to those without, leading to a net reduction in species diversification (the interplay of speciation and extinction). In contrast, the use of warning coloration and mimicry was associated with higher rates of speciation, but unchanged rates of extinction.

There are a number of plausible reasons why the use of chemical defense might lead to higher extinction rates. For example, it could be that there is trade off which leaves prey vulnerable to other kinds of enemies, such as infectious diseases, but we don't yet understand what drives the relationship.

The results of the study are only partially consistent with a long-held hypothesis, called 'escape-and-radiate', which predicts that effective defenses let prey escape from predators and diversify into many different species in the process.

We've shown that this hypothesis, which is widely cited and used, requires some revision because of its failure to account for the effects of extinction rates. We propose that 'escape-and-radiate' should be seen as just one part of a more general hypothesis for the macroevolutionary effects of antipredator defense that includes both speciation and extinction. In addition, our findings could help support the conservation of endangered species by allowing some predictability of extinction risk from knowledge of antipredator defenses. Amphibians are a key example of this as they have suffered population declines worldwide, including many of the iconic poison-dart frogs.

Wednesday, October 21, 2015

The Earth's evolutionary history is threatened by species loss in the current sixth mass extinction event in Earth's history. Such extinction events not only eliminate species but also their unique evolutionary histories. Here we review the expected loss of Earth's evolutionary history quantified by phylogenetic diversity (PD) and evolutionary distinctiveness (ED) at risk.

I came across this interesting publication recently and I find the idea intriguing. A number of colleagues is arguing for a while already that it is important to in quantify the loss not only of species but also of evolutionary history because it might capture the diversity of life better than simple measures of taxonomic richness.

The paper reviews the state of current knowledge on the loss of evolutionary history. The authors review and assess common indices used to quantify evolutionary history and its loss. They also have a closer look at evolutionary history at risk from human impacts and how well it is protected by current conservation practices.

Due to the general paucity of data, global evolutionary history losses have been predicted for only a few groups, such as mammals, birds, amphibians, plants, corals and fishes. Among these groups, there is now empirical support that extinction threats are clustered on the phylogeny; however this is not always a sufficient condition to cause higher loss of phylogenetic diversity in comparison to a scenario of random extinctions. Extinctions of the most evolutionarily distinct species and the shape of phylogenetic trees are additional factors that can elevate losses of evolutionary history. Consequently, impacts of species extinctions differ among groups and regions, and even if global losses are low within large groups, losses can be high among subgroups or within some regions.

The study also shows that evolutionary history is poorly protected by current conservation practices. Although there is a chance that it is indirectly protected by current conservation schemes, it needs optimization by integrating phylogenetic indices with those that capture rarity and extinction risk. The paper shows a potential approach to this by using both PD and ED and ways to quantify loss for both utilizing a species' IUCN threat status.

The authors repeatedly argue that data availability and quality, in particular, on species phylogenetic relationships and extinction probabilities are key to proper predictions of PD and ED loss. I agree with them that important progress has been made and I think that the large amount of DNA barcode data could be much more utilized. PD of barcode sequences for example has been used a few times calculate accumulation curves to determine completeness of sampling.

Of course, there is no such thing as enough data but some of the remaining challenges actually lie in the evaluation of a threat status for data-deficient species. Such improvements could provide more complete and accurate predictions paving a way for phylogenetic diversity and evolutionary distinctiveness to become part of routine conservation practices.

Tuesday, October 20, 2015

Despite knowledge on invasive species’ predatory effects, we know little of their influence as prey. Non-native prey should have a neutral to positive effect on native predators by supplementing the prey base. However, if non-native prey displace native prey, then an invader's net influence should depend on both its abundance and value relative to native prey.

In order to quantify the effect of non-native prey on native predator populations US researchers conducted a meta-analysis by reviewing 109 studies covering the interactions of 47 different prey species and 93 predator species.

The research shows that predators benefit most from eating invasive prey only if their traditional food sources remain intact - that is, if they are able to maintain their usual diet and eat invaders only as an occasional snack. Predator populations increased as much as 57 percent after an invasion of new prey but only when native prey remained abundant as well.

Eating non-native prey isn't as good for predators as eating native prey. It may be that the new prey isn't as nutritious, or that the predator hasn't evolved the ability to eat or digest it well. But in all these studies, whenever predators' diets were restricted to non-native prey, the predators did not perform as well as they did on native prey. We only saw a benefit to the predator when the non-native prey provided a supplemental food source.

There are also examples of success stories involving predators and invasive prey. For example, the Lake Erie water snake was endangered, but its status was recently upgraded in part because it adapted to feed on the round goby, an invasive bottom-feeding fish from Europe. Another case might be the common mud crabs in the southeastern United States which are studied by the publication authors. the crabs might be developing a taste for the green porcelain crab, a relatively recently arrived invasive species. Such a switch to the super-abundant green porcelain crab could alter the mud crabs' overall community structure.

We want to caution that while we might see an increase in population abundance and density among some native predator species, that's not always a good thing, either. There could be unintended consequences for other native species.

Monday, October 19, 2015

Metrics that synthesize the complex effects of climate change are essential tools for mapping future threats to biodiversity and predicting which species are likely to adapt in place to new climatic conditions, disperse and establish in areas with newly suitable climate, or face the prospect of extirpation.

In a study published this week researchers have used high-performance computing methods and comprehensive data on the distribution of thousands of species to map the threat that climate change poses to birds, mammals and amphibians across the Western Hemisphere. They searched for and categorized millions of images, using approaches similar to those developed for facial and fingerprint recognition software. This allowed them to sift through millions of pixels representing future climate at different locations to determine each site's current climate fingerprint.

By incorporating data on the climate tolerances of individual species, the researchers were able to fine-tune their initial estimates of dispersal based on climate change alone. This combination of climate data and biological data showed that although polar regions currently are experiencing the greatest shifts in climate, species in the Amazon basin face the greatest threats because of the narrow range of conditions they can tolerate and the longer distance to cooler habitat that can serve as climate refuges.

These results suggest that tropical species will likely be some of the most vulnerable to climate change. While we know that many of these species are restricted to relatively narrow climatic ranges, combining this information with detailed maps of where and how climate is shifting most rapidly provides a much clearer picture of where threats are greatest.

As climate shifts over the coming decades, such "velocity of climate change" information can help predict which species are likely to adapt in place to new climatic conditions, disperse and establish in areas with newly suitable climate, or face the prospect of extinction. It would allow us to estimate the actual distance and speed it would take for an animal to disperse across the landscape to stay within its climate tolerances and survive in the face of climate change. For example, the Amazon's yellow-banded poison dart frog is projected to have to move several hundreds of kilometers to the southwest, because most of its range will likely become unsuitable for this species to live. Several other amphibian species in this region show similar movement patterns.

This study is the first time that scientists have been able to accurately estimate the velocity of climate change for thousands of species over entire continents. Even as governments step up their commitment to reduce future greenhouse gas emissions, this information can help planners identify climate refuges where conservation would reduce loss of species from the climate change that is already locked into the system from past emissions.

Friday, October 16, 2015

Here is another round of talented nature photographers with a liking for creatures with more than four legs.

The first one is Paul Bertner who calls himself a Pengembara, a word in Malay which means a kind of traveler, adventurer, backpacker, vagabond- all the above. You can find more about him and his travels on his blog. I picked the caterpillar photo there as well but Paul also has a Flickr site.

This bald-faced hornet was photographed by Sean McCann from Vancouver. He is a biologist and amateur photographer. He writes on his website: I wrote my thesis on Red-throated Caracara foraging biology, having spent 5 seasons in French Guiana studying these fascinating birds. I have also studied social wasp defensive behavior and have worked on mosquito reproductive ecology. There are a lot of great images on his Flickr site as well.

When talking about insect photographers one should not forget one of the masters of the trade - Alex Wild. His macro photos are perhaps the best known and most widely distributed of all. His photographs appear in numerous natural history museums, magazines, books, television programs, and other media. Alex is a Texas-based entomologist who started photographing insects more than a decade ago. He shares his knowledge on the web and offers courses and workshops. As for the quality of his work, well, just have a look at the emerging Aedes aegypti I picked.

Yudy Saw claims he is doing insect macro photography just as a hobby but my, these details are just amazing and he certainly has an eye for rare circumstances. Probably one of his most famous images showing a mantis with a spider on its head was featured in the Telegraph. Yudy is from Banten, Indonesia and you can find a lot of his work on his 500px site. Below you can watch a slide show with some of his insect close ups.

Time to find some vertebrates for future posts - fish in particular, just for more balance.

Thursday, October 15, 2015

We've long known that biodiversity has a stabilizing effect on productivity over time. But we haven't been quite sure whether that's during extreme events, after them, or both. This research showed that diverse communities are more stable because they exhibit resistance during extreme climate events.

In 1994 a study reported that ecosystem productivity of diverse grassland plant communities was more resilient to a major drought than that of less diverse communities. However, this study had not experimentally manipulated biodiversity, which made is very difficult to disentangle biodiversity variation and other parameters such as variation in species composition and resource availability. Unfortunately, many studies over the last two decades did not help to sufficiently answer the question whether biodiversity buffers ecosystems against climate extremes, which are becoming increasing frequent worldwide.

A new study involved more than three dozen researchers from the U.S., Germany, the U.K., Ireland, France, Switzerland, the Netherlands, Czech Republic and Japan. The researchers began by classifying each year of each experiment on a five-point scale from extremely dry to extremely wet. They then measured corresponding productivity - basically, how much above-ground plant material each level of plant biodiversity produced each year. The group did 46 experiments in which they manipulated grassland plant diversity and measured productivity across Europe and North America.

Combining results across the 46 study sites, the researchers found that the higher the plant biodiversity, the lower the variability in productivity during wet or dry climate events. Overall, productivity of communities with only one or two species changed an average of 50 percent during events, while those with 16 to 32 species changed only half that much. Biodiversity did not, however, seem to strongly influence how quickly a site returned to normal productivity after wet or dry events.

Wednesday, October 14, 2015

Hexapoda, the insects and their relatives, includes over half of all described species. Because large proportions of this diversity cluster within a small set of phytophagous groups, dietary substrates have been proposed to shape patterns of richness within the clade through antagonistic coevolution and zones of ecological opportunity.

For a long time the richness of the insect has been regarded as linked with their plant-feeding habits especially when unusually species rich were compared with their nearest relatives. Researchers have often been intrigued by the fact there are some incredibly rich plant-feeding insect groups, while other groups are not so diverse. This might be also only half the truth as many large scale DNA Barcoding programs show that groups thought to be species-poor contain a large number of cryptic species waiting to be discovered and described.

We wanted to explore how species are distributed between different insect groups, because not all groups of insects are species rich. What kinds of groups are rich should tell you why they are. We found that there is not a consistent association between plant feeding and high species richness, which was a bit of a surprise. We coded all the different groups for what they feed on and then looked more closely at which diets are consistently associated with higher or lower richness.
It turns out that different diets evolved at different times in evolutionary history and are gained and lost at different rates. This might be a possible explanation as to why some dietary options are connected to very species rich groups. However, it seems that this is not caused by general differences in the rate at which they diversify.More likely there is a complex relationship between diet and the rate of diversification. It might be that to become very species rich on a particular diet, you need to use a particular kind of niche, or you need a particular adaptation that other groups don't have. This more complex picture is going to take a lot of working out.

Thursday, October 8, 2015

If you think about it, you're driving around the suburban environment, and every time a new development goes in, you have a lot of decision making happening as to what plant species are going to be planted around those properties. If we do all that landscaping with non-native plants, are we limiting the wildlife and conservation support system that could be available within that given plot of land? What the gardens we constructed for the study are trying to replicate are landscaping decisions that people might make if they wanted to support native insect communities that in turn support much of the diversity around us.

Researchers of the University of Delaware tried to understand how the composition of the plants that homeowners plant in their yards affects herbivore communities. To conduct the study, they planted imitation yards with different common gardens of both native and non-native tree species and collected data over a three-year period, determining the herbivore communities and species found on those plants. They compared native trees to non-native trees that had no close native relative and to non-natives that are closely related to the native community.

Within the distantly related group, they found that herbivores were less diverse when they looked at individual non-native tree species, and as they moved from one non-native tree species to another, they found similar species of herbivores using those trees. Non-native plants reduced the diversity of insect populations in gardens, even when these non-native plants are closely related to the native plants.

You get this compounding effect where you have a lower diversity of herbivores per tree but then you also are getting more similar species as you move between trees species and among sites, so you end up with even less diverse communities than you would expect. There is this group of species of non-natives that do not have any close native relatives at all. These non-natives support more generalized and redundant herbivore communities than the native plants that they're potentially replacing on landscapes.

Wednesday, October 7, 2015

The tropical plant Vismia baccifera protects itself by producing a number of repellent chemicals, including three compounds that are toxic to living cells. Few plant-eating insects can stomach such a cocktail, but for those that can, the advantages are clear - less competition for a meal, and a chemical toolkit they can use in their own defense.

One of them is the skipper butterfly Pyrrhopyge thericles. Their caterpillars only eat plants of the genus Vismia. In contrast the caterpillars of the large saturniid, Periphoba arcaei, have a much broader diet, including Vismia plants and many others. The caterpillars of both species are brightly coloured, one with conspicuous stripes, and the other blue-green with bristles. For potential predators such flashy looks are associated with toxicity. Now it would seem that the skipper butterfly that exclusively consumed plants containing toxic chemicals would more easily incorporate toxins into its body than the one with a broad diet.

A new study by the Smithsonian Tropical Research Institute (STRI) in Panama found the opposite. They compared the diets of the caterpillars of the two species at several life stages and tested for the presence and concentration of plant toxins called vismiones. While two vismione compounds are found at a ratio of 1:6 in the plants, in the specialist butterfly caterpillars the compounds were barely detectable, and at roughly equal ratios. Meanwhile, the generalist moth caterpillars contained significant quantities of the rarer of the two compounds, suggesting that they were able to actively store this plant chemical in their own bodies. Both caterpillars' fecal matter revealed a 1:2 ratio of the plant compounds, indicating that their bodies might uptake compounds selectively or convert molecules of one type over the other.

We know very little about just how each plant-eating insect handles these chemicals--how they store them or eliminate them. Some insects might isolate the compounds so they do not cause them harm, while others might convert the molecules into forms that are harder to detect. Insects that process harmful toxins without damaging their own cells have a survival advantage. For a generalist species, the ability to sequester toxic compounds might be an early evolutionary breakthrough, the first step along the pathway to becoming a toxic plant specialist.

Tuesday, October 6, 2015

Every day, hundreds of different plant species -- many of them listed as invasive -- are traded online worldwide on auction platforms. This exacerbates the problem of uncontrollable biological invasions as they are often introduced as ornamental plants. Those in turn spread into the wild, where they now threaten the native flora. The vast majority of invasive species can be easily obtained with just a click of the mouse.

For 50 days, the researchers tracked which plant species were offered for sale in various countries, and how often. They used a software specifically developed for the study taking advantage of the fact that all online platforms make sale listings accessible to external software build to systematically search for and analyse online content. All findings were crosschecked against common lists of invasive plants, established by various institutions such as the International Union for the Conservation of Nature (IUCN).

Over the course of the study the colleagues found 2,625 different plant species offered for sale on eBay. Of those, 510 are known to be invasive in at least one region of the world. And out of that group, 35 are on the IUCN's list of the 100 worst invasive species.

These are astonishing numbers and sellers found in the study were located in 65 countries. Offers to sell invasive species came from 55 of these countries, including Australia. Dealers there offer invasive plants - that are known to be harmful in other parts of the world - on a grand scale. That was unexpected, since the Australians don't allow you to bring any invasive plants across their borders. But surprisingly, there are apparently no controls in place to make sure potentially harmful plants don't leave the continent.

Rules governing the trade in these plants are halfheartedly enforced, if at all. And it's virtually impossible for the dealers to keep track of all the laws and regulations concerning import and export of potential invasive species in different countries. A new threat is also emerging: regions that previously had no access to trade flows can now participate thanks to the internet. South Africa is now showing up on our map. We have no idea whether the plants that are being put on the global market from this corner of world will prove to be invasive species. It may well be that several of them could become invasive in other regions.

The only way to contain invasions is by limiting and monitoring the trade. The study shows that it is theoretically possible to continuously monitor this trade in order to spot newly traded species, which could signal future invasions. Many countries already have sets of rules and regulations in place with the goal of curbing the spread of invasive species.

As online trade blossoms, it makes it even more urgent for the authorities to take action or for responsible large commercial nurseries to adjust their product ranges.

Monday, October 5, 2015

Type specimens have high scientific importance because they provide the only certain connection between the application of a Linnean name and a physical specimen. Many other individuals may have been identified as a particular species, but their linkage to the taxon concept is inferential. Because type specimens are often more than a century old and have experienced conditions unfavorable for DNA preservation, success in sequence recovery has been uncertain.

Earlier studies have shown that standard molecular methods can also be applied to type material of soft-bodied insects but success is rather mixed. Dried, mounted specimens can yield viable DNA even over 100 years after collection from as little as a single leg. Past studies usually included a number of PCR reactions to generate a set of short amplicons which could be assembled into a barcode contig. The problem is that templates can be depleted before the full sequence is recovered especially when many amplification reactions are required. This is extremely problematic if only one type specimen for a species is available.

In a new study coming out of BIO my colleagues used multiplex PCR to generate short amplicons covering the barcode region and then Next Generation Sequencing (NGS) for their characterization. They started with conventional Sanger sequencing of 1820 type specimens of the moth family Geometridae from the Natural History Museum,London as part of a project to develop a strongly validated taxonomic system to support species inventories and studies of host plant use in Papua New Guinea. For their comparative NGS run the colleagues picked single representatives from 30 different genera of the family, all between 102 and 123 years old.

They were able to recover sequence information from all specimens with average read lengths ranging from 458bp to 610bp which is impressive. But the inevitable question is if such an approach is not cost-prohibitive at this point. This is what the study authors have to say and I find that very encouraging:

By sequencing ten specimens in each NGS run, costs were similar to Sanger analysis. Future increases in the number of specimens processed in each run promise substantial reductions in cost, making it possible to anticipate a future where barcode sequences are available from most type specimens.

Friday, October 2, 2015

I am a big fan of crowd sourced funding and in the past few years a couple of really good research programs could be started using such a large community based resource. For that reason and because I know both researcher and proposed research location I am happy to support a UC San Diego project by spreading the word through this blog.

Yesterday, Heather Henter from the Natural Reserve System group at the UCSD wrote to me (and I believe to many, many others): My students and I are working on an effort to document biodiversity at the Scripps Coastal Reserve, a UC nature reserve adjacent to campus. The students are a group of spider enthusiasts that are using DNA barcoding to identify and inventory all of the spider species at the reserve. This is really important because the diversity of little animals like insects and spiders is so poorly known and because San Diego is such a hotspot of endangered biodiversity. There are a lot of species that only occur here, and a lot of habitat that is disappearing. We think that the first step to conserving biodiversity is just knowing what is there! We hope you can help us, or pass along our video to others that might be interested.

No problem, consider it done:

Are you interested in supporting Heather and her students to build a DNA Barcode reference library? Here is how.

Thursday, October 1, 2015

Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools.

The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. The three key objectives of PESI include standardisation in taxonomic reference systems, enhancement of the quality and completeness of taxonomic data sets and creation of integrated access to taxonomic information. The five pillars of biological community networks, Zoology, Botany, Marine Biota, Mycology and Phycology, have been integrated in five infrastructural components: knowledge, consensus, standards, data and dissemination.

Scientific names are key carriers of biodiversity information. Therefore, for the efficient exploring and integration of biodiversity data, the development of a functional taxonomic resolution system, including the establishment of a shared taxonomic standard (as a core component), is essential for all sorts of biodiversity assessments. PESI provides such an infrastructure for Europe, integrating the relevant technical (informatics) and social (knowledge & users) networks into a common work program, serving a wide community of biodiversity workers